A Database of Aquatic animals' Transcriptome Map

Change organism database
dbATM

dbATM is a database resource for Aquatic Animals' Transcriptome that understanding gene, gene expression and high-level functions, such as the Gene Ontology, KEGG Pathway, and Cluster of Orthologous Group.

Next-generation sequencing (NGS) technologies have been used to reveal the complex and dynamic gene expression through RNA sequencing (RNA-seq). De novo assembly of transcriptome were used to uncover the specific gene and gene regulatory network for the non-model organisms. However the access to these transcriptomes tends to be limited, we hereby provide the first database specific for Aquatic Animals' Transcriptome Map, dbATM. Also, to improve the assembly quality, we developed an assembly approach consist of three common assembly tools (Oases, SOAPdenovo-Trans, and Trinity), with another tool called cd-hit-est used to merged these three assembly results. We also provide different scenarios and exhaustive functional analysis such as proteins (blast against Swiss-Prot protein database by blastx), conserved domains (blast against Conserved Domains Database, CDD by RPSblast), gene ontology and systems biology KEGG pathways annotations. dbATM provides a systematic approach for data mining from aquatic animals' transcriptome, with a web-based and user friendly interface.



Select Species






Species No. of Bases Platform Read Type Link
Anguilla japonica
Japanese eel
8.61 G Illumina HiSeq 2000 PE, 2x101 Taxonomy
Wikipedia
Astyanax mexicanus
Blind cave fish
8.88 G Illumina HiSeq 2000 PE, 2x100 Source
Taxonomy
Wikipedia
Clupea harengus
Atlantic herring
11.72 G Illumina HiSeq 2000 PE, 2x101 Source
Taxonomy
Wikipedia
Crassostrea gigas
Pacific oyster
Tissue or Condition: optimal salinity stress
2.86 G Illumina HiSeq 2000 PE, 2x93 Source
Taxonomy
Wikipedia
Fundulus grandis
Gulf killifish
5.00 G Illumina Genome Analyzer IIx PE, 2x60 Source
Taxonomy
Wikipedia
Gasterosteus aculeatus
Three-spined stickleback
Tissue or Condition: muscle
3.20 G Illumina HiSeq 2000 PE, 2x101 Source
Taxonomy
Wikipedia
Ictalurus punctatus
Channel catfish
4.96 G Illumina HiSeq 2000 PE, 2x101 Source
Taxonomy
Wikipedia
Lateolabrax japonicus
Suzuki
2.59 G Illumina Genome Analyzer II PE, 2x75 Source
Taxonomy
Wikipedia
Microphysogobio brevirostris 4.84 G Illumina HiSeq 2000 PE, 2x90 Taxonomy
Wikipedia
Mytilus galloprovincialis
Mediterranean mussel
1.37 G Illumina Genome Analyzer II PE, 2x100 Source
Taxonomy
Wikipedia
Neocaridina denticulata
Shrimp
6.06 G Illumina HiSeq 2000 PE, 2x101 Taxonomy
Wikipedia
Pandalus latirostris
Hokkai shrimp
Tissue or Condition: NTK
4.74 G Illumina Genome Analyzer II PE, 2x76 Source
Taxonomy
Wikipedia
Penaeus monodon
Indian black tiger shrimp
5.60 G Illumina Genome Analyzer II PE, 2x72 Source
Taxonomy
Wikipedia
Planorbarius corneus
Apple snial
5.66 G Illumina HiSeq 2000 PE, 2x101 Taxonomy
Wikipedia
Plecoglossus altivelis
Ayu
4.48 G Illumina HiSeq 2000 PE, 2x90 Source
Taxonomy
Wikipedia
Poecilia formosa
Amazon molly
5.72 G Illumina HiSeq 2000 PE, 2x100 Source
Taxonomy
Wikipedia
Poecilia mexicana
Shortfin molly
Tissue or Condition: gill
1.63 G Illumina HiSeq 2000 PE, 2x101 Source
Taxonomy
Wikipedia
Protopterus annectens
West African lungfish
Tissue or Condition: liver
1.94 G Illumina HiSeq 2000 PE, 2x76 Source
Taxonomy
Wikipedia
Pundamilia nyererei 2.10 G Illumina HiSeq 2000 PE, 2x76 Source
Taxonomy
Wikipedia
Sinocyclocheilus angustiporus
Surfacefish
Tissue or Condition: Brain
1.10 G Illumina Genome Analyzer II PE, 2x74 Source
Taxonomy
Wikipedia
Sinocyclocheilus anophthalmus
Cavefish
Tissue or Condition: Brain
2.06 G Illumina Genome Analyzer II PE, 2x74 Source
Taxonomy
Wikipedia
Tetraodon nigroviridis
Green spotted puffer
Tissue or Condition: brain
11.43 G Illumina HiSeq 2000 PE, 2x76 Source
Taxonomy
Wikipedia
Total 22 Species 106.55 G

Citing dbATM

C.H. Chou, H.Y. Huang, W.C. Huang, S.D. Hsu, C.D. Hsiao, C.Y. Liu, Y.H. Chen, Y.C. Liu, W.Y. Huang, M.L. Lee, Y.C. Chen, and H.D. Huang* "The Aquatic Animals' Transcriptome Resource for Comparative Functional Analysis" (2018) BMC Genomics, 19(Suppl 2):103


Recent News
June 30th, 2013: dbATM 1.0.0